Package psidev.psi.mi.jami.xml.model.extension.xml300

Class XmlAllostery

java.lang.Object

psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlCooperativeEffect

psidev.psi.mi.jami.xml.model.extension.xml300.XmlAllostery

All Implemented Interfaces:

com.sun.xml.bind.Locatable, FileSourceContext, Allostery<AllostericEffector>, CooperativeEffect

public class XmlAllostery
extends AbstractXmlCooperativeEffect
implements Allostery<AllostericEffector>

XML 3.0 implementation of Allostery

Since:

15/11/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Nested Class Summary

Nested classes/interfaces inherited from class psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlCooperativeEffect

AbstractXmlCooperativeEffect.JAXBAffectedInteractionRefWrapper, AbstractXmlCooperativeEffect.JAXBAttributeWrapper, AbstractXmlCooperativeEffect.JAXBCooperativityEvidenceWrapper

Field Summary

Fields inherited from interface psidev.psi.mi.jami.model.CooperativeEffect

AFFECTED_INTERACTION, AFFECTED_INTERACTION_ID, ALLOSTERIC_DYNAMIC_CHANGE, ALLOSTERIC_DYNAMIC_CHANGE_ID, ALLOSTERIC_EFFECTOR, ALLOSTERIC_EFFECTOR_ID, ALLOSTERIC_K_RESPONSE, ALLOSTERIC_K_RESPONSE_ID, ALLOSTERIC_MOLECULE, ALLOSTERIC_MOLECULE_ID, ALLOSTERIC_PTM, ALLOSTERIC_PTM_ID, ALLOSTERIC_STRUCTURE_CHANE, ALLOSTERIC_STRUCTURE_CHANE_ID, ALLOSTERIC_V_RESPONSE, ALLOSTERIC_V_RESPONSE_ID, ALLOSTERY, ALLOSTERY_ID, ALTERED_PHYSICO_COMPATIBILITY, ALTERED_PHYSICO_COMPATIBILITY_ID, BINDING_HIDING, BINDING_HIDING_ID, COMPOSITE_BINDING, COMPOSITE_BINDING_ID, COOPERATIVE_EFFECT_VALUE, COOPERATIVE_EFFECT_VALUE_ID, EFFECT_OUTCOME, EFFECT_OUTCOME_MI, HETEROTROPIC_ALLOSTERY, HETEROTROPIC_ALLOSTERY_ID, HOMOTROPIC_ALLOSTERY, HOMOTROPIC_ALLOSTERY_ID, NEGATIVE_EFFECT, NEGATIVE_EFFECT_ID, PARTICIPANT_REF, PARTICIPANT_REF_ID, POSITIVE_EFFECT, POSITIVE_EFFECT_ID, PRE_ORGANIZATION, PRE_ORGANIZATION_ID, PREASSEMBLY, PREASSEMBLY_ID

Constructor Summary

Constructors

Constructor	Description
XmlAllostery()	Constructor for XmlAllostery.
XmlAllostery(CvTerm outcome)	Constructor for XmlAllostery.
XmlAllostery(CvTerm outcome, CvTerm response)	Constructor for XmlAllostery.

Method Summary

Modifier and Type	Method	Description
AllostericEffector	getAllostericEffector()	getAllostericEffector.
CvTerm	getAllostericMechanism()	Getter for the field allostericMechanism.
ModelledEntity	getAllostericMolecule()	Getter for the field allostericMolecule.
CvTerm	getAllosteryType()	Getter for the field allosteryType.
protected void	initialiseDefaultAllostericEffector()	initialiseDefaultAllostericEffector.
void	setAllostericEffector(AllostericEffector effector)	Sets the effector that elicits an allosteric response.
void	setAllostericMechanism(CvTerm mechanism)	Sets the allosteric mechanism.
void	setAllostericMolecule(ModelledEntity participant)	Sets the allosteric molecule.
void	setAllosteryType(CvTerm type)	Sets the allostery type.
void	setJAXBAllostericMechanism(XmlCvTerm mechanism)	setJAXBAllostericMechanism.
void	setJAXBAllostericMoleculeRef(int ref)	setJAXBAllostericMoleculeRef.
void	setJAXBAllosteryType(XmlCvTerm type)	setJAXBAllosteryType.
void	setJAXBFeatureEffectorRef(int effector)	setJAXBFeatureEffectorRef.
void	setJAXBMoleculeEffectorRef(int effector)	setJAXBMoleculeEffectorRef.
String	toString()	toString

Methods inherited from class psidev.psi.mi.jami.xml.model.extension.xml300.AbstractXmlCooperativeEffect

addAffectedInteractionRef, getAffectedInteractions, getAnnotations, getCooperativityEvidences, getOutCome, getResponse, getSourceLocator, initialiseAffectedInteractions, initialiseAnnotations, initialiseCooperativityEvidences, setJAXBAffectedInteractionWrapper, setJAXBAttributeWrapper, setJAXBCooperativityEvidenceWrapper, setJAXBOutCome, setJAXBResponse, setOutCome, setResponse, setSourceLocation, setSourceLocator, sourceLocation

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface psidev.psi.mi.jami.model.CooperativeEffect

getAffectedInteractions, getAnnotations, getCooperativityEvidences, getOutCome, getResponse, setOutCome, setResponse

Constructor Detail

XmlAllostery

public XmlAllostery()

Constructor for XmlAllostery.

XmlAllostery

public XmlAllostery(CvTerm outcome)

Constructor for XmlAllostery.

Parameters:

outcome - a CvTerm object.

XmlAllostery

public XmlAllostery(CvTerm outcome,
                    CvTerm response)

Constructor for XmlAllostery.

Parameters:

outcome - a CvTerm object.

response - a CvTerm object.

Method Detail

toString

public String toString()

toString

Specified by:

toString in interface FileSourceContext

Overrides:

toString in class AbstractXmlCooperativeEffect

Returns:

the file source context as a String. If the source locator is not null, it should give the source locator properties

getAllostericMechanism

public CvTerm getAllostericMechanism()

Getter for the field allostericMechanism.

Specified by:

getAllostericMechanism in interface Allostery<AllostericEffector>

Returns:

a CvTerm object.

setAllostericMechanism

public void setAllostericMechanism(CvTerm mechanism)

Sets the allosteric mechanism.

Specified by:

setAllostericMechanism in interface Allostery<AllostericEffector>

Parameters:

mechanism - : allosteric mechanism

getAllosteryType

public CvTerm getAllosteryType()

Getter for the field allosteryType.

Specified by:

getAllosteryType in interface Allostery<AllostericEffector>

Returns:

a CvTerm object.

setAllosteryType

public void setAllosteryType(CvTerm type)

Sets the allostery type.

Specified by:

setAllosteryType in interface Allostery<AllostericEffector>

Parameters:

type - : allostery type

getAllostericMolecule

public ModelledEntity getAllostericMolecule()

Getter for the field allostericMolecule.

Specified by:

getAllostericMolecule in interface Allostery<AllostericEffector>

Returns:

a ModelledEntity object.

setAllostericMolecule

public void setAllostericMolecule(ModelledEntity participant)

Sets the allosteric molecule.

Specified by:

setAllostericMolecule in interface Allostery<AllostericEffector>

Parameters:

participant - : allosteric molecule (can refer to any participating entity)

getAllostericEffector

public AllostericEffector getAllostericEffector()

getAllostericEffector.

Specified by:

getAllostericEffector in interface Allostery<AllostericEffector>

Returns:

a AllostericEffector object.

initialiseDefaultAllostericEffector

protected void initialiseDefaultAllostericEffector()

initialiseDefaultAllostericEffector.

setAllostericEffector

public void setAllostericEffector(AllostericEffector effector)

Sets the effector that elicits an allosteric response.

Specified by:

setAllostericEffector in interface Allostery<AllostericEffector>

Parameters:

effector - : the allosteric effector

setJAXBAllostericMoleculeRef

public void setJAXBAllostericMoleculeRef(int ref)

setJAXBAllostericMoleculeRef.

Parameters:

ref - a int.

setJAXBMoleculeEffectorRef

public void setJAXBMoleculeEffectorRef(int effector)

setJAXBMoleculeEffectorRef.

Parameters:

effector - a int.

setJAXBFeatureEffectorRef

public void setJAXBFeatureEffectorRef(int effector)

setJAXBFeatureEffectorRef.

Parameters:

effector - a int.

setJAXBAllostericMechanism

public void setJAXBAllostericMechanism(XmlCvTerm mechanism)

setJAXBAllostericMechanism.

Parameters:

mechanism - a XmlCvTerm object.

setJAXBAllosteryType

public void setJAXBAllosteryType(XmlCvTerm type)

setJAXBAllosteryType.

Parameters:

type - a XmlCvTerm object.